Variant report

Variant	rs9929358
Chromosome Location	chr16:70827888-70827889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70820987..70825073-chr16:70825115..70829640,4	MCF-7	breast:
2	chr16:70825645..70828535-chr16:70829296..70832343,3	MCF-7	breast:
3	chr16:70824598..70831036-chr16:70832753..70836225,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000103043	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13339117	0.81[AFR][1000 genomes]
rs1770429	0.95[YRI][hapmap]
rs28605599	0.85[AFR][1000 genomes]
rs4985364	0.96[YRI][hapmap]
rs55789619	0.84[AFR][1000 genomes]
rs59236367	0.85[AMR][1000 genomes]
rs59924713	0.85[AMR][1000 genomes]
rs7185508	0.86[YRI][hapmap]
rs7188712	0.91[YRI][hapmap]
rs7194197	1.00[MEX][hapmap]
rs8045407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8051921	0.94[AFR][1000 genomes]
rs8058702	0.92[ASW][hapmap];0.86[LWK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv1061191	chr16:70754975-71201367	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1059478	chr16:70773597-71237055	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	esv2758429	chr16:70807122-71316983	Active TSS ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
7	esv2758653	chr16:70807122-71316983	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
8	nsv916160	chr16:70809280-71120138	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9929358	VAC14	cis	multi-tissue	Pritchard
rs9929358	VAC14	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70785800-70828000	Strong transcription	Primary T cells from cord blood	blood
2	chr16:70805200-70834000	Weak transcription	Fetal Heart	heart
3	chr16:70807400-70833800	Weak transcription	Fetal Brain Male	brain
4	chr16:70817400-70832600	Weak transcription	Small Intestine	intestine
5	chr16:70818000-70833000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr16:70818200-70832600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:70818400-70832600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr16:70818400-70833400	Weak transcription	HUVEC	blood vessel
9	chr16:70819000-70833400	Weak transcription	K562	blood
10	chr16:70819200-70833000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr16:70819400-70832800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr16:70819400-70833600	Weak transcription	NHDF-Ad	bronchial
13	chr16:70819400-70833800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr16:70819800-70833400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr16:70820000-70833400	Weak transcription	HSMMtube	muscle
16	chr16:70820200-70832400	Weak transcription	Fetal Brain Female	brain
17	chr16:70820200-70833200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr16:70820200-70833200	Weak transcription	Brain Substantia Nigra	brain
19	chr16:70820200-70833400	Weak transcription	Esophagus	oesophagus
20	chr16:70820200-70833400	Weak transcription	NHLF	lung
21	chr16:70820200-70833600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr16:70820200-70833800	Weak transcription	Brain Hippocampus Middle	brain
23	chr16:70820200-70834000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr16:70820400-70832600	Weak transcription	Brain Anterior Caudate	brain
25	chr16:70820400-70833000	Weak transcription	HMEC	breast
26	chr16:70820400-70833200	Weak transcription	Brain Angular Gyrus	brain
27	chr16:70820400-70833800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr16:70820400-70834000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr16:70820400-70834000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr16:70820400-70834200	Weak transcription	Colonic Mucosa	Colon
31	chr16:70820400-70834200	Weak transcription	Left Ventricle	heart
32	chr16:70820400-70834200	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr16:70820400-70834400	Weak transcription	Aorta	Aorta
34	chr16:70820600-70831000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr16:70820600-70832400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr16:70820600-70833400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr16:70820600-70833400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr16:70820600-70833600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr16:70820600-70833600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr16:70820800-70830000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr16:70820800-70832800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:70820800-70833200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr16:70820800-70833200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr16:70820800-70833400	Weak transcription	NHEK	skin
45	chr16:70820800-70833600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr16:70820800-70834200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr16:70821000-70833000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr16:70821000-70833200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr16:70821200-70832200	Weak transcription	Adipose Nuclei	Adipose
50	chr16:70821200-70833000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links